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Yorodumi- EMDB-0542: Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0542 | ||||||||||||
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Title | Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1 (OA-1) | ||||||||||||
Map data | Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1 (OA-1) | ||||||||||||
Sample |
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Function / homology | Function and homology information cell outer membrane / toxin activity / periplasmic space / cell surface / extracellular region Similarity search - Function | ||||||||||||
Biological species | Helicobacter pylori (bacteria) / Campylobacter pylori (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Zhang K / Zhang H / Li S / Au S / Chiu W | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Cryo-EM structures of vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution. Authors: Kaiming Zhang / Huawei Zhang / Shanshan Li / Grigore D Pintilie / Tung-Chung Mou / Yuanzhu Gao / Qinfen Zhang / Henry van den Bedem / Michael F Schmid / Shannon Wing Ngor Au / Wah Chiu / Abstract: Human gastric pathogen () is the primary risk factor for gastric cancer and is one of the most prevalent carcinogenic infectious agents. Vacuolating cytotoxin A (VacA) is a key virulence factor ...Human gastric pathogen () is the primary risk factor for gastric cancer and is one of the most prevalent carcinogenic infectious agents. Vacuolating cytotoxin A (VacA) is a key virulence factor secreted by and induces multiple cellular responses. Although structural and functional studies of VacA have been extensively performed, the high-resolution structure of a full-length VacA protomer and the molecular basis of its oligomerization are still unknown. Here, we use cryoelectron microscopy to resolve 10 structures of VacA assemblies, including monolayer (hexamer and heptamer) and bilayer (dodecamer, tridecamer, and tetradecamer) oligomers. The models of the 88-kDa full-length VacA protomer derived from the near-atomic resolution maps are highly conserved among different oligomers and show a continuous right-handed β-helix made up of two domains with extensive domain-domain interactions. The specific interactions between adjacent protomers in the same layer stabilizing the oligomers are well resolved. For double-layer oligomers, we found short- and/or long-range hydrophobic interactions between protomers across the two layers. Our structures and other previous observations lead to a mechanistic model wherein VacA hexamer would correspond to the prepore-forming state, and the N-terminal region of VacA responsible for the membrane insertion would undergo a large conformational change to bring the hydrophobic transmembrane region to the center of the oligomer for the membrane channel formation. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0542.map.gz | 203.9 MB | EMDB map data format | |
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Header (meta data) | emd-0542-v30.xml emd-0542.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_0542.png | 50.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0542 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0542 | HTTPS FTP |
-Validation report
Summary document | emd_0542_validation.pdf.gz | 433.2 KB | Display | EMDB validaton report |
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Full document | emd_0542_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | emd_0542_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_0542_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0542 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0542 | HTTPS FTP |
-Related structure data
Related structure data | 6nyfMC 0543C 0544C 0545C 0546C 0547C 0548C 0549C 0550C 0551C 6nygC 6nyjC 6nylC 6nymC 6nynC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10607 (Title: Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A (VacA) oligomeric assemblies Data size: 3.9 TB Data #1: Helicobacter pylori vacuolating cytotoxin A [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0542.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1 (OA-1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1...
Entire | Name: Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1 (OA-1) |
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Components |
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-Supramolecule #1: Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1...
Supramolecule | Name: Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 1 (OA-1) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: 60190 |
Molecular weight | Experimental: 88 KDa |
-Macromolecule #1: Vacuolating cytotoxin autotransporter
Macromolecule | Name: Vacuolating cytotoxin autotransporter / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Campylobacter pylori (bacteria) |
Molecular weight | Theoretical: 88.463211 KDa |
Sequence | String: AFFTTVIIPA IVGGIATGTA VGTVSGLLGW GLKQAEEANK TPDKPDKVWR IQAGKGFNEF PNKEYDLYKS LLSSKIDGGW DWGNAATHY WIKGGQWNKL EVDMKDAVGT YKLSGLRNFT GGDLDVNMQK ATLRLGQFNG NSFTSYKDSA DRTTRVDFNA K NILIDNFL ...String: AFFTTVIIPA IVGGIATGTA VGTVSGLLGW GLKQAEEANK TPDKPDKVWR IQAGKGFNEF PNKEYDLYKS LLSSKIDGGW DWGNAATHY WIKGGQWNKL EVDMKDAVGT YKLSGLRNFT GGDLDVNMQK ATLRLGQFNG NSFTSYKDSA DRTTRVDFNA K NILIDNFL EINNRVGSGA GRKASSTVLT LQASEGITSS KNAEISLYDG ATLNLASNSV KLNGNVWMGR LQYVGAYLAP SY STINTSK VTGEVNFNHL TVGDHNAAQA GIIASNKTHI GTLDLWQSAG LNIIAPPEGG YKDKPNNTPS QSGAKNDKQE SSQ NNSNTQ VINPPNSTQK TEVQPTQVID GPFAGGKDTV VNIDRINTKA DGTIKVGGFK ASLTTNAAHL NIGKGGVNLS NQAS GRTLL VENLTGNITV DGPLRVNNQV GGYALAGSSA NFEFKAGVDT KNGTATFNND ISLGRFVNLK VDAHTANFKG IDTGN GGFN TLDFSGVTNK VNINKLITAS TNVAVKNFNI NELIVKTNGV SVGEYTHFSE DIGSQSRINT VRLETGTRSI FSGGVK FKS GEKLVIDEFY YSPWNYFDAR NIKNVEITRK FASSTPENPW GTSKLMFNNL TLGQNAVMDY SQFSNLTIQG DFINNQG TI NYLVRGGKVA TLNVGNAAAM MFNNDIDSAT GFYKPLIKIN SAQDLIKNTE HVLLKAKIIG YGNVSTGTNG ISNVNLEE Q FKERLALYNN NNRMDTCVVR NTDDIKACGM AIGNQSMVNN PDNYKYLIGK AWKNIGISKT ANGSKISVYY LGNSTPTEN GGNTTNLPTN TTNNARFASY A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | VacA OA-1 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 3 / Number real images: 13708 / Average exposure time: 6.0 sec. / Average electron dose: 7.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: BACKBONE TRACE |
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Output model | PDB-6nyf: |